diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -2,6 +2,10 @@ ## [Unreleased] +## [0.1.3.1] - 2020-04-02 +### Fixed +- Reading of insertion code for residues in MAE. + ## [0.1.3.0] - 2020-03-27 ### Added - Residue index in `Structure`. diff --git a/cobot-io.cabal b/cobot-io.cabal --- a/cobot-io.cabal +++ b/cobot-io.cabal @@ -1,140 +1,136 @@ cabal-version: 1.12 - --- This file has been generated from package.yaml by hpack version 0.31.2. --- --- see: https://github.com/sol/hpack --- --- hash: a5a2fbb335e61a22b55a3d74cd08557730ea19a8b93005c693a4576dad82e498 - -name: cobot-io -version: 0.1.3.0 -synopsis: Biological data file formats and IO -description: Please see the README on GitHub at -category: Bio -homepage: https://github.com/less-wrong/cobot-io#readme -bug-reports: https://github.com/less-wrong/cobot-io/issues -author: Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov -maintainer: pavel@yakovlev.me -copyright: 2018-2019, Less Wrong Bio -license: BSD3 -license-file: LICENSE -build-type: Simple +name: cobot-io +version: 0.1.3.1 +license: BSD3 +license-file: LICENSE +copyright: 2018-2019, Less Wrong Bio +maintainer: pavel@yakovlev.me +author: Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov +homepage: https://github.com/less-wrong/cobot-io#readme +bug-reports: https://github.com/less-wrong/cobot-io/issues +synopsis: Biological data file formats and IO +description: + Please see the README on GitHub at +category: Bio +build-type: Simple extra-source-files: README.md ChangeLog.md source-repository head - type: git - location: https://github.com/less-wrong/cobot-io + type: git + location: https://github.com/less-wrong/cobot-io library - exposed-modules: - Bio.ABI - Bio.ABI.Clean - Bio.ABI.Decode - Bio.FASTA - Bio.FASTA.Parser - Bio.FASTA.Type - Bio.FASTA.Writer - Bio.GB - Bio.GB.Parser - Bio.GB.Type - Bio.GB.Writer - Bio.MAE - Bio.MAE.Parser - Bio.MAE.Type - Bio.MMTF - Bio.MMTF.Decode - Bio.MMTF.Decode.Codec - Bio.MMTF.Decode.MessagePack - Bio.MMTF.MessagePack - Bio.MMTF.Type - Bio.PDB - Bio.PDB.BondRestoring - Bio.PDB.Functions - Bio.PDB.Parser - Bio.PDB.Reader - Bio.PDB.Type - Bio.Sequence - Bio.Sequence.Basecalled - Bio.Sequence.Basecalled.Type - Bio.Sequence.Class - Bio.Sequence.Functions.Marking - Bio.Sequence.Functions.Sequence - Bio.Sequence.Functions.Weight - Bio.Sequence.Utilities - Bio.Structure - Bio.Structure.Functions - Bio.Uniprot - Bio.Uniprot.Parser - Bio.Uniprot.Type - other-modules: - Paths_cobot_io - hs-source-dirs: - src - default-extensions: DeriveGeneric DeriveFunctor DeriveFoldable DeriveAnyClass FlexibleInstances InstanceSigs MultiParamTypeClasses RecordWildCards ScopedTypeVariables OverloadedStrings TypeApplications TypeFamilies DataKinds ConstraintKinds TypeOperators TemplateHaskell FlexibleContexts - build-depends: - array >=0.5 && <0.6 - , attoparsec >=0.10 && <0.14 - , base >=4.7 && <5 - , binary >=0.8.3.0 && <1.0 - , bytestring >=0.10.8.1 && <0.11 - , containers >=0.5.7.1 && <0.7 - , data-msgpack >=0.0.9 && <0.1 - , deepseq >=1.4 && <1.5 - , http-conduit >=2.3 && <2.4 - , hyraxAbif >=0.2.3.15 && <0.2.4.0 - , lens >=4.16 && <5.0 - , linear >=1.20 && <1.21 - , mtl >=2.2.1 && <2.3.0 - , split - , text >=1.2.2.1 && <1.3 - , vector - default-language: Haskell2010 + exposed-modules: + Bio.ABI + Bio.ABI.Clean + Bio.ABI.Decode + Bio.FASTA + Bio.FASTA.Parser + Bio.FASTA.Type + Bio.FASTA.Writer + Bio.GB + Bio.GB.Parser + Bio.GB.Type + Bio.GB.Writer + Bio.MAE + Bio.MAE.Parser + Bio.MAE.Type + Bio.MMTF + Bio.MMTF.Decode + Bio.MMTF.Decode.Codec + Bio.MMTF.Decode.MessagePack + Bio.MMTF.MessagePack + Bio.MMTF.Type + Bio.PDB + Bio.PDB.BondRestoring + Bio.PDB.Functions + Bio.PDB.Parser + Bio.PDB.Reader + Bio.PDB.Type + Bio.Sequence + Bio.Sequence.Basecalled + Bio.Sequence.Basecalled.Type + Bio.Sequence.Class + Bio.Sequence.Functions.Marking + Bio.Sequence.Functions.Sequence + Bio.Sequence.Functions.Weight + Bio.Sequence.Utilities + Bio.Structure + Bio.Structure.Functions + Bio.Uniprot + Bio.Uniprot.Parser + Bio.Uniprot.Type + hs-source-dirs: src + other-modules: + Paths_cobot_io + default-language: Haskell2010 + default-extensions: DeriveGeneric DeriveFunctor DeriveFoldable + DeriveAnyClass FlexibleInstances InstanceSigs MultiParamTypeClasses + RecordWildCards ScopedTypeVariables OverloadedStrings + TypeApplications TypeFamilies DataKinds ConstraintKinds + TypeOperators TemplateHaskell FlexibleContexts + build-depends: + array ==0.5.*, + attoparsec >=0.10 && <0.14, + base >=4.7 && <5, + binary >=0.8.3.0 && <1.0, + bytestring >=0.10.8.1 && <0.11, + containers >=0.5.7.1 && <0.7, + data-msgpack >=0.0.9 && <0.1, + deepseq ==1.4.*, + http-conduit ==2.3.*, + hyraxAbif >=0.2.3.15 && <0.2.4.0, + lens >=4.16 && <5.0, + linear ==1.20.*, + mtl >=2.2.1 && <2.3.0, + split >=0.2.3.3 && <0.3, + text >=1.2.2.1 && <1.3, + vector >=0.12.0.3 && <0.13 test-suite cobot-io-test - type: exitcode-stdio-1.0 - main-is: Spec.hs - other-modules: - ABISpec - FastaParserSpec - FASTASpec - FastaWriterSpec - GBParserSpec - GBWriterSpec - MAEParserSpec - MAESpec - MMTFSpec - PDBParserSpec - PDBSpec - SequenceSpec - StructureSpec - UniprotSpec - Paths_cobot_io - hs-source-dirs: - test - default-extensions: OverloadedStrings TypeFamilies - ghc-options: -threaded -rtsopts -with-rtsopts=-N - build-depends: - QuickCheck >=2.9.2 && <2.14 - , array >=0.5 && <0.6 - , attoparsec >=0.10 && <0.14 - , base >=4.7 && <5 - , binary >=0.8.3.0 && <1.0 - , bytestring >=0.10.8.1 && <0.11 - , cobot-io - , containers >=0.5.7.1 && <0.7 - , data-msgpack >=0.0.9 && <0.1 - , deepseq >=1.4 && <1.5 - , directory - , hspec >=2.4.1 && <2.8 - , http-conduit >=2.3 && <2.4 - , hyraxAbif >=0.2.3.15 && <0.2.4.0 - , lens >=4.16 && <5.0 - , linear >=1.20 && <1.21 - , mtl >=2.2.1 && <2.3.0 - , neat-interpolation >=0.3 - , split - , text >=1.2.2.1 && <1.3 - , vector - default-language: Haskell2010 + type: exitcode-stdio-1.0 + main-is: Spec.hs + hs-source-dirs: test + other-modules: + ABISpec + FastaParserSpec + FASTASpec + FastaWriterSpec + GBParserSpec + GBWriterSpec + MAEParserSpec + MAESpec + MMTFSpec + PDBParserSpec + PDBSpec + SequenceSpec + StructureSpec + UniprotSpec + Paths_cobot_io + default-language: Haskell2010 + default-extensions: OverloadedStrings TypeFamilies + ghc-options: -threaded -rtsopts -with-rtsopts=-N + build-depends: + QuickCheck >=2.9.2 && <2.14, + array ==0.5.*, + attoparsec >=0.10 && <0.14, + base >=4.7 && <5, + binary >=0.8.3.0 && <1.0, + bytestring >=0.10.8.1 && <0.11, + cobot-io -any, + containers >=0.5.7.1 && <0.7, + data-msgpack >=0.0.9 && <0.1, + deepseq ==1.4.*, + directory >=1.3.3.0 && <1.4, + hspec >=2.4.1 && <2.8, + http-conduit ==2.3.*, + hyraxAbif >=0.2.3.15 && <0.2.4.0, + lens >=4.16 && <5.0, + linear ==1.20.*, + mtl >=2.2.1 && <2.3.0, + neat-interpolation ==0.3.*, + split >=0.2.3.3 && <0.3, + text >=1.2.2.1 && <1.3, + vector >=0.12.0.3 && <0.13 diff --git a/src/Bio/MAE.hs b/src/Bio/MAE.hs --- a/src/Bio/MAE.hs +++ b/src/Bio/MAE.hs @@ -140,7 +140,7 @@ where name = stripQuotes $ unsafeGetFromContents "s_m_pdb_residue_name" h residueNumber = unsafeGetFromContents "i_m_residue_number" h - insertionCode = unsafeGetFromContents "s_m_insertion_code" h + insertionCode = getFromContents defaultInsertionCode "s_m_insertion_code" h atoms = V.fromList $ fmap indexToAtom group localInds = [0 .. length group - 1] diff --git a/test/PDBSpec.hs b/test/PDBSpec.hs --- a/test/PDBSpec.hs +++ b/test/PDBSpec.hs @@ -145,5 +145,4 @@ firstMaeModel :: (MonadIO m) => FilePath -> m Model firstMaeModel filepath = do eitherMae <- modelsFromMaeFile filepath - -- `evaluate . force` fails for some reason - pure . V.head $ fromRight undefined eitherMae + liftIO . ef . V.head $ fromRight undefined eitherMae